Molecule Design Support Apparatus and Computer-Readable Storage Medium

1. A molecule design support apparatus comprising: a storage part configured to store, with respect to data having a given three-dimensional molecular structure, an atom data structure A related to an atom, a bond axis data structure B related to a bond axis, and a molecule data structure M related to a molecule; wherein the atom data structure A includes an identification number “a” made up of an atomic sequence number in internal coordinates, an atom number made up of a chemical symbol, a bond axis number made up of a numerical value that varies when an arbitrary new molecular structure is added to an original molecule, an identification number of the bond axis, made up of a set data of an identification number “b” of each bond axis included in the bond axis number, and an identification flag for use in checking whether or not the molecular structure has a ring structure, wherein the bond axis data structure B includes an identification number “b” made up of the number that is necessary to make all of the bond axes correspond 1:1 with each other, an identification number of a terminal atom, made up of a set data of the identification number “a” of the atom existing at both terminals of the bond axis, and having a data number is 2, an event flag indicating a present type of event with respect to events of the molecular structure forming a GUI (Graphical User Interface), including a rotation operation, an expansion and contraction operation, a delete operation, an add operation and a replace operation, an identification flag identical to the identification flag of the atom data structure A, and vector information including information indicating a 1:1 correspondence between the bond axis and a three-dimensional vector, wherein the molecule data structure M includes the atom number, the bond axis number, the atom data structure A, the bond axis data structure B, event information of the event, and the event flag, an input part; a display configured to display on a screen thereof the three-dimensional molecular structure by a half vector format or a ball-and-stick format; a determining part configured to determine, in the molecular structure, an end that is to become a target of a coordinate modification with respect to a molecule in its entirety, in response to a bond axis of the molecule specified from the input part; a modifying part configured to make a modification of the molecular structure based on the specified bond axis and the end that is the target of the coordinate modification, using information included in the atom data structure A and the bond axis data structure B, in response to the modification specified from the input part, said modification including at least one of a free rotation around an atom, a rotation around a bond axis, an angular modification between two axes, a modification of a dihedral angle, and an expansion and contraction of a bond axis; and a display part configured to display a modified molecular structure on the screen of the display based on a determination made by the determining part and the modification made by the modifying part.

2. The molecule design support apparatus as claimed in claim 1 , wherein: said determining part determines the end that is to become the target of the coordinate modification with respect to the molecule in its entirety, based on one bond axis of the molecule or, said one bond axis and one of two terminal atoms of said one bond axis specified from the input part; and said modifying part makes the free rotation around the atom by an angle specified from the input part, by making a free rotation around an atom located on an end, of the specified bond axis, other than the target of the coordinate modification, based on said one bond axis or, said one bond axis and one of two terminal atoms of said one bond axis in the ball-and-stick format.

3. The molecule design support apparatus as claimed in claim 1 , wherein: said determining part determines the end that is to become the target of the coordinate modification with respect to the bond axis, based on one bond axis of the molecule or, said one bond axis and one of two terminal atoms of said one bond axis in the ball-and-stick format specified from the input part; and said modifying part makes the rotation around the specified bond axis by an angle specified from the input part, by making the rotation around the specified bond axis, based on said one bond axis or, said one bond axis and said one of the two terminal atoms of said one bond axis.

4. The molecule design support apparatus as claimed in claim 1 , wherein: said determining part determines the end that is to become the target of the coordinate modification with respect to the molecule in its entirety, based on two continuous bond axes of the molecule or, said two continuous bond axes and one of two terminal atoms of said two continuous bond axes in the ball-and-stick format specified from the input part; and said modifying part makes a modification of the angle between two specified bond axes by an angle specified from the input part, by modifying an angle between said two continuous bond axes, based on said two continuous bond axes or, said two continuous bond axes and one of the two terminal atoms of said two continuous bond axes in the ball-and-stick format.

5. The molecule design support apparatus as claimed in claim 1 , wherein: said determining part determines the end that is to become the target of the coordinate modification with respect to the molecule in its entirety, based on three continuous bond axes of the molecule or, said three continuous bond axes and one of two terminal atoms of said three continuous bond axes in the ball-and-stick format specified from the input part; and said modifying part makes a rotation of the dihedral angle around a center bond axis of the three specified continuous bond axes by an angle specified from the input part, by rotating the center bond axis of said three continuous bond axes, based on said three continuous bond axes or, said three continuous bond axes and one of the two terminal atoms of said three continuous bond axes in the ball-and-stick format.

6. The molecule design support apparatus as claimed in claim 1 , wherein: said determining part determines the end that is to become the target of the coordinate modification with respect to the bond axis, based on one bond axis of the molecule or, said one bond axis and one of two terminal atoms of said one bond axis in the ball-and-stick format specified from the input part; and said modifying part makes an expansion and contraction of the specified bond axis by a contraction scale specified from the input part, based on said one bond axis or, said one bond axis and one of the two terminal atoms of said one bond axis in the ball-and-stick format.

7. The molecule design support apparatus as claimed in claim 1 , wherein said determining part sets, as the target of the coordinate modification, only a bond axis set having a smaller bond axis number, from among a plurality of bond axis sets including bond axes linked to a bond axis other than the specified bond axis, with respect to two terminal atoms of the specified bond axis, when only the bond axis or continuous bond axes are specified from the input part.

8. The molecule design support apparatus as claimed in claim 1 , wherein said determining part sets, as the target of the coordinate modification, only a bond axis set including bond axes linked to a bond axis other than the specified bond axis using a specified atom or an atom that is not specified as a base point, when the bond axis or continuous bond axes are specified from the input part and one of two terminal atoms of the specified bond axis is further specified from the input part.

9. The molecule design support apparatus as claimed in claim 1 , wherein said determining part excludes from the target of the coordinate modification a bond axis set including bond axes linked to a bond axis other than the specified bond axis with respect to one of two terminal atoms of the bond axis or continuous bond axes specified from the input part, when the bond axis set includes a bond axis linked to a bond axis other than the specified bond axis with respect to the other terminal atom of the bond axis or continuous bond axes specified from the input part.

10. A non-transitory computer-readable storage medium which stores a program for causing a computer, having an input part, to realize a molecule design support function, said program comprising: a storing procedure causing the computer to store in a storage part, with respect to data having a given three-dimensional molecular structure, an atom data structure A related to an atom, a bond axis data structure B related to a bond axis, and a molecule data structure M related to a molecule; wherein the atom data structure A includes an identification number “a” made up of an atomic sequence number in internal coordinates, an atom number made up of a chemical symbol, a bond axis number made up of a numerical value that varies when an arbitrary new molecular structure is added to an original molecule, an identification number of the bond axis, made up of a set data of an identification number “b” of each bond axis included in the bond axis number, and an identification flag for use in checking whether or not the molecular structure has a ring structure, wherein the bond axis data structure B includes an identification number “b” made up of the number that is necessary to make all of the bond axes correspond 1:1 with each other, an identification number of a terminal atom, made up of a set data of the identification number “a” of the atom existing at both terminals of the bond axis, and having a data number is 2, an event flag indicating a present type of event with respect to events of the molecular structure forming a GUI (Graphical User Interface), including a rotation operation, an expansion and contraction operation, a delete operation, an add operation and a replace operation, an identification flag identical to the identification flag of the atom data structure A, and vector information including information indicating a 1:1 correspondence between the bond axis and a three-dimensional vector, wherein the molecule data structure M includes the atom number, the bond axis number, the atom data structure A, the bond axis data structure B, event information of the event, and the event flag, a determining procedure causing the computer to determine, in the three-dimensional molecular structure that is displayed by a half vector format or a ball-and-stick format on a screen of a display, an end that is to become a target of a coordinate modification with respect to a molecule in its entirety, in response to a bond axis of the molecule specified from the input part; a modifying procedure causing the computer to make a modification of the molecular structure based on the specified bond axis and the end that is the target of the coordinate modification, using information included in the atom data structure A and the bond axis data structure B, in response to the modification specified from the input part, said modification including at least one of a free rotation around an atom, a rotation around a bond axis, an angular modification between two axes, a modification of a dihedral angle, and an expansion and contraction of a bond axis; and a display procedure causing the computer to display a modified molecular structure on the screen of the display based on a determination made by the determining procedure and the modification made by the modifying procedure.

11. The non-transitory computer-readable storage medium as claimed in claim 10 , wherein: said determining procedure causes the computer to determine the end that is to become the target of the coordinate modification with respect to the molecule in its entirety, based on one bond axis of the molecule or, said one bond axis and one of two terminal atoms of said one bond axis specified from the input part; and said modifying procedure causes the computer to make the free rotation around the atom by an angle specified from the input part, by making a free rotation around an atom located on an end, of the specified bond axis, other than the target of the coordinate modification, based on said one bond axis or, said one bond axis and one of two terminal atoms of said one bond axis in the ball-and-stick format.

12. The non-transitory computer-readable storage medium as claimed in claim 10 , wherein: said determining procedure causes the computer to determine the end that is to become the target of the coordinate modification with respect to the bond axis, based on one bond axis of the molecule or, said one bond axis and one of two terminal atoms of said one bond axis in the ball-and-stick format specified from the input part; and said modifying procedure causes the computer to make the rotation around the specified bond axis by an angle specified from the input part, by making the rotation around the specified bond axis, based on said one bond axis or, said one bond axis and said one of the two terminal atoms of said one bond axis.

13. The non-transitory computer-readable storage medium as claimed in claim 10 , wherein: said determining procedure causes the computer to determine the end that is to become the target of the coordinate modification with respect to the molecule in its entirety, based on two continuous bond axes of the molecule or, said two continuous bond axes and one of two terminal atoms of said two continuous bond axes in the ball-and-stick format specified from the input part; and said modifying procedure causes the computer to make a modification of the angle between two specified bond axes by an angle specified from the input part, by modifying an angle between said two continuous bond axes, based on said two continuous bond axes or, said two continuous bond axes and one of the two terminal atoms of said two continuous bond axes in the ball-and-stick format.

14. The non-transitory computer-readable storage medium as claimed in claim 10 , wherein: said determining procedure causes the computer to determine the end that is to become the target of the coordinate modification with respect to the molecule in its entirety, based on three continuous bond axes of the molecule or, said three continuous bond axes and one of two terminal atoms of said three continuous bond axes in the ball-and-stick format specified from the input part; and said modifying procedure causes the computer to make a rotation of the dihedral angle around a center bond axis of the three specified continuous bond axes by an angle specified from the input part, by rotating the center bond axis of said three continuous bond axes, based on said three continuous bond axes or, said three continuous bond axes and one of the two terminal atoms of said three continuous bond axes in the ball-and-stick format.

15. The non-transitory computer-readable storage medium as claimed in claim 10 , wherein: said determining procedure causes the computer to determine the end that is to become the target of the coordinate modification with respect to the bond axis, based on one bond axis of the molecule or, said one bond axis and one of two terminal atoms of said one bond axis in the ball-and-stick format specified from the input part; and said modifying procedure causes the computer to make an expansion and contraction of the specified bond axis by a contraction scale specified from the input part, based on said one bond axis or, said one bond axis and one of the two terminal atoms of said one bond axis in the ball-and-stick format.

16. The non-transitory computer-readable storage medium as claimed in claim 10 , wherein said determining procedure causes the computer to set, as the target of the coordinate modification, only a bond axis set having a smaller bond axis number, from among a plurality of bond axis sets including bond axes linked to a bond axis other than the specified bond axis, with respect to two terminal atoms of the specified bond axis, when only the bond axis or continuous bond axes are specified from the input part.

17. The non-transitory computer-readable storage medium as claimed in claim 10 , wherein said determining procedure causes the computer to set, as the target of the coordinate modification, only a bond axis set including bond axes linked to a bond axis other than the specified bond axis using a specified atom or an atom that is not specified as a base point, when the bond axis or continuous bond axes are specified from the input part and one of two terminal atoms of the specified bond axis is further specified from the input part.

18. The non-transitory computer-readable storage medium as claimed in claim 10 , wherein said determining procedure causes the computer to exclude from the target of the coordinate modification a bond axis set including bond axes linked to a bond axis other than the specified bond axis with respect to one of two terminal atoms of the bond axis or continuous bond axes specified from the input part, when the bond axis set includes a bond axis linked to a bond axis other than the specified bond axis with respect to the other terminal atom of the bond axis or continuous bond axes specified from the input part.